QPCR: Application for real-time PCR data management and analysis

BACKGROUND: Since its introduction quantitative real-time polymerase chain reaction (qPCR) has become the standard method for quantification of gene expression. Its high sensitivity, large dynamic range, and accuracy led to the development of numerous applications with an increasing number of samples to be analyzed. Data analysis consists of a number of steps, which have to be carried out in several different applications. Currently, no single tool is available which incorporates storage, management, and multiple methods covering the complete analysis pipeline. RESULTS: QPCR is a versatile web-based Java application that allows to store, manage, and analyze data from relative quantification qPCR experiments. It comprises a parser to import generated data from qPCR instruments and includes a variety of analysis methods to calculate cycle-threshold and amplification efficiency values. The analysis pipeline includes technical and biological replicate handling, incorporation of sample or gene specific efficiency, normalization using single or multiple reference genes, inter-run calibration, and fold change calculation. Moreover, the application supports assessment of error propagation throughout all analysis steps and allows conducting statistical tests on biological replicates. Results can be visualized in customizable charts and exported for further investigation. CONCLUSION: We have developed a web-based system designed to enhance and facilitate the analysis of qPCR experiments. It covers the complete analysis workflow combining parsing, analysis, and generation of charts into one single application. The system is freely available a

Drawing OWL 2 ontologies with Eddy the editor

In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments. This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification

Development of a Custom Call Management System for the Service Department of Premiere Copier Inc.

Premiere Copier needs a system that will facilitate the functionality required by the current business process as well as being more robust, reliable and scalable. The new system has to mitigate all the problem areas mentioned in the section 1.2.3. The complete list of the requirements is presented in the Section 3.1.1. This project is the first real life experience for the one man developing team as well. Working through the whole development life cycle of the application, fulfilling the roles of project manager, developer and designer at the same time presents an excellent educational opportunity as well

Project Venezia-Gondola (A Framework for P-Commerce)

A novel project named Venezia-Gondola (Project V-G) was presented, which describes an application platform that enables the activities of Peer-to-Peer commerce (P-Commerce). A new pattern called the Inverted Model-View-Controller (IMVC) pattern was claimed that is suitable for P-Commerce. The author also explains the principles of the Project V-G and possible architecture for future development

Instantiating the PERFORM system architecture for industrial case studies

The PERFoRM project, an innovation action promoted within the scope of the EU Horizon 2020 program, advocates the use of an Industrie 4.0 compliant system architecture for the seamless reconfiguration of robots and machinery. The system architecture re-uses the innovative results from previous successful R & D projects on distributed control systems domain, such as SOCRADES, IMC-AESOP, GRACE and IDEAS. This paper, after describing the main pillars of the PERFoRM system architecture, focuses on mapping the system architecture into four industrial use cases aiming to validate the system architecture design before its deployment in the real environments.info:eu-repo/semantics/publishedVersio

Customizable Feature based Design Pattern Recognition Integrating Multiple Techniques

Die Analyse und Rückgewinnung von Architekturinformationen aus existierenden Altsystemen ist eine komplexe, teure und zeitraubende Aufgabe, was der kontinuierlich steigenden Komplexität von Software und dem Aufkommen der modernen Technologien geschuldet ist. Die Wartung von Altsystemen wird immer stärker nachgefragt und muss dabei mit den neuesten Technologien und neuen Kundenanforderungen umgehen können. Die Wiederverwendung der Artefakte aus Altsystemen für neue Entwicklungen wird sehr bedeutsam und überlebenswichtig für die Softwarebranche. Die Architekturen von Altsystemen unterliegen konstanten Veränderungen, deren Projektdokumentation oft unvollständig, inkonsistent und veraltet ist. Diese Dokumente enthalten ungenügend Informationen über die innere Struktur der Systeme. Häufig liefert nur der Quellcode zuverlässige Informationen über die Struktur von Altsystemen. Das Extrahieren von Artefakten aus Quellcode von Altsystemen unterstützt das Programmverständnis, die Wartung, das Refactoring, das Reverse Engineering, die nachträgliche Dokumentation und Reengineering Methoden. Das Ziel dieser Dissertation ist es Entwurfsinformationen von Altsystemen zu extrahieren, mit Fokus auf die Wiedergewinnung von Architekturmustern. Architekturmuster sind Schlüsselelemente, um Architekturentscheidungen aus Quellcode von Altsystemen zu extrahieren. Die Verwendung von Mustern bei der Entwicklung von Applikationen wird allgemein als qualitätssteigernd betrachtet und reduziert Entwicklungszeit und kosten. In der Vergangenheit wurden unterschiedliche Methoden entwickelt, um Muster in Altsystemen zu erkennen. Diese Techniken erkennen Muster mit unterschiedlicher Genauigkeit, da ein und dasselbe Muster unterschiedlich spezifiziert und implementiert wird. Der Lösungsansatz dieser Dissertation basiert auf anpassbaren und wiederverwendbaren Merkmal-Typen, die statische und dynamische Parameter nutzen, um variable Muster zu definieren. Jeder Merkmal-Typ verwendet eine wählbare Suchtechnik (SQL Anfragen, Reguläre Ausdrücke oder Quellcode Parser), um ein bestimmtes Merkmal eines Musters im Quellcode zu identifizieren. Insbesondere zur Erkennung verschiedener Varianten eines Musters kommen im entwickelten Verfahren statische, dynamische und semantische Analysen zum Einsatz. Die Verwendung unterschiedlicher Suchtechniken erhöht die Genauigkeit der Mustererkennung bei verschiedenen Softwaresystemen. Zusätzlich wurde eine neue Semantik für Annotationen im Quellcode von existierenden Softwaresystemen entwickelt, welche die Effizienz der Mustererkennung steigert. Eine prototypische Implementierung des Ansatzes, genannt UDDPRT, wurde zur Erkennung verschiedener Muster in Softwaresystemenen unterschiedlicher Programmiersprachen (JAVA, C/C++, C#) verwendet. UDDPRT erlaubt die Anpassung der Mustererkennung durch den Benutzer. Alle Abfragen und deren Zusammenspiel sind konfigurierbar und erlauben dadurch die Erkennung von neuen und abgewandelten Mustern. Es wurden umfangreiche Experimente mit diversen Open Source Software Systemen durchgeführt und die erzielten Ergebnisse wurden mit denen anderer Ansätze verglichen. Dabei war es möglich eine deutliche Steigerung der Genauigkeit im entwickelten Verfahren gegenüber existierenden Ansätzen zu zeigen.Recovering design information from legacy applications is a complex, expensive, quiet challenging, and time consuming task due to ever increasing complexity of software and advent of modern technology. The growing demand for maintenance of legacy systems, which can cope with the latest technologies and new business requirements, the reuse of artifacts from the existing legacy applications for new developments become very important and vital for software industry. Due to constant evolution in architecture of legacy systems, they often have incomplete, inconsistent and obsolete documents which do not provide enough information about the structure of these systems. Mostly, source code is the only reliable source of information for recovering artifacts from legacy systems. Extraction of design artifacts from the source code of existing legacy systems supports program comprehension, maintenance, code refactoring, reverse engineering, redocumentation and reengineering methodologies. The objective of approach used in this thesis is to recover design information from legacy code with particular focus on the recovery of design patterns. Design patterns are key artifacts for recovering design decisions from the legacy source code. Patterns have been extensively tested in different applications and reusing them yield quality software with reduced cost and time frame. Different techniques, methodologies and tools are used to recover patterns from legacy applications in the past. Each technique recovers patterns with different precision and recall rates due to different specifications and implementations of same pattern. The approach used in this thesis is based on customizable and reusable feature types which use static and dynamic parameters to define variant pattern definitions. Each feature type allows user to switch/select between multiple searching techniques (SQL queries, Regular Expressions and Source Code Parsers) which are used to match features of patterns with source code artifacts. The technique focuses on detecting variants of different design patterns by using static, dynamic and semantic analysis techniques. The integrated use of SQL queries, source code parsers, regular expressions and annotations improve the precision and recall for pattern extraction from different legacy systems. The approach has introduced new semantics of annotations to be used in the source code of legacy applications, which reduce search space and time for detecting patterns. The prototypical implementation of approach, called UDDPRT is used to recognize different design patterns from the source code of multiple languages (Java, C/C++, C#). The prototype is flexible and customizable that novice user can change the SQL queries and regular expressions for detecting implementation variants of design patterns. The approach has improved significant precision and recall of pattern extraction by performing experiments on number of open source systems taken as baselines for comparisons

Doctor of Philosophy

dissertationClinical research plays a vital role in producing knowledge valuable for understanding human disease and improving healthcare quality. Human subject protection is an obligation essential to the clinical research endeavor, much of which is governed by federal regulations and rules. Institutional Review Boards (IRBs) are responsible for overseeing human subject research to protect individuals from harm and to preserve their rights. Researchers are required to submit and maintain an IRB application, which is an important component in the clinical research process that can significantly affect the timeliness and ethical quality of the study. As clinical research has expanded in both volume and scope over recent years, IRBs are facing increasing challenges in providing efficient and effective oversight. The Clinical Research Informatics (CRI) domain has made significant efforts to support various aspects of clinical research through developing information systems and standards. However, information technology use by IRBs has not received much attention from the CRI community. This dissertation project analyzed over 100 IRB application systems currently used at major academic institutions in the United States. The varieties of system types and lack of standardized application forms across institutions are discussed in detail. The need for building an IRB domain analysis model is identified. . iv In this dissertation, I developed an IRB domain analysis model with a special focus on promoting interoperability among CRI systems to streamline the clinical research workflow. The model was evaluated by a comparison with five real-world IRB application systems. Finally, a prototype implementation of the model was demonstrated by the integration of an electronic IRB system with a health data query system. This dissertation project fills a gap in the research of information technology use for the IRB oversight domain. Adoption of the IRB domain analysis model has potential to enhance efficient and high-quality ethics oversight and to streamline the clinical research workflow

A Taxonomy of Internet Appliances

The world is evolving from one in which almost all access to the Internet comes from personal computers (PCs) to one in which so-called Internet appliances (IAs) will make up a greater share of end-user equipment. Today's PC is a general-purpose, highly configurable and extensible device ? an "intelligent end-node" of the sort the Internet's designers had in mind. As such, it allows users much freedom of choice (such as which service provider to use, which Web sites to visit, and which new software to download) in exchange for dealing with associated complexity. An IA is a device connected to the Internet, but beyond that there is little consensus on functionality and target markets. There is, however, general agreement that it reduces the level of complexity seen by the user. A variety of approaches to reducing complexity are being pursued. These fall on a spectrum from totally fixing the function of devices, to automating the configuration of more general purpose systems. In the middle are devices whose functions appear more or less fixed to the user, but which retain some limited capability for upgrade through their Internet connection